AquaMine

NCBI (RefSeq) genes are available for all AquaMine species. Check the Data Source page for the availability of Ensembl genes.

Query for genes:

• Gene    Transcripts + Exons
• Gene    GO Terms
• Gene    Symbol + Description
• Gene    Protein Sequences
• Chromosomal location    Genes
• Gene    Chromosomal location
• Gene    Coding Sequences
• Transcript    Gene

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Query for expression:

• Gene ID    Gene Expression Levels
• Tissue and Organism    Gene Expression Levels
• Experiment    Gene Expression Levels
• Organism    Experiments and Tissues

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Most protein information is from UniProt and InterPro. NCBI (RefSeq) and Ensembl protein ids and sequences are also available.

Query for proteins:

• Organism    All UniProt Proteins
• Gene    Protein Sequences
• Transcript    Protein
• Gene    Proteins (UniProt)
• Organism    Proteins (UniProt) and Publications

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AquaMine includes orthologue predictions from three sources: OrthoDB v10.1, AquaMine-Ortho, and Ensembl (from Ensembl Compara and Ensembl Metazoa). The AquaMine-Ortho dataset was computed using the Orthologer pipeline (developed by OrthoDB). Both AquaMine-Ortho and Ortho-DB use RefSeq gene ids; the Ensembl data set uses Ensembl gene ids. AquaMine-Ortho includes all AquaMine species, while OrthoDB v10.1 and Ensembl each include a subset species (see Data Source page). The Ensembl dataset provides pairwise orthologue relationships, and classifies them as ortholog_one2one, ortholog_many2many, ortholog_one2many. OrthoDB and AquaMine-Ortho provide orthologous groups that are descended from a single ancestral gene, based on a specified last common ancestral taxon. Any orthologous group from either data source can include in-paralogues, which result from gene duplication after divergence from the last common ancestor. Click on the Taxonomy tab in the main navigation bar above to view the taxonomy tree and the last common ancestral groups used in AquaMine-Ortho.

Query for homology:

• Gene ID    Homologues (OrthoDB or AquaMine-Ortho)
• Orthologue Cluster ID    Genes
• Gene ID    Homologues (Ensembl)    GO Terms
• Gene ID    Homologues (OrthoDB or AquaMine-Ortho)    GO Terms
• Gene ID    Homologues (OrthoDB or AquaMine-Ortho) from specified Organism
• Gene ID    Homologues (Ensembl)
• Organism    Homologues
• Gene ID    Reciprocal Best Hits

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Gene Ontology annotation is from UniProt. Pathway datasets are from KEGG.

Query for function:

• Gene    GO Terms
• Gene    Pathways
• Gene    Description, Symbol and GO Terms
• Gene ID    Homologues (Ensembl)    GO Terms
• GO Term    Genes
• Gene ID    Homologues (OrthoDB or AquaMine-Ortho)    GO Terms
• Gene ID    Homologues    Pathways
• GO Term    GO Name

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These template queries allow retrieval of an entire dataset for a specified organism or gene set.

Query for entire gene set:

• Gene Source and Organism    Genes
• All Genes    Database Cross References
• Genome Assembly    Chromosome IDs
• Organism    Transcripts + Genes + Database Cross References
• Organism    Proteins (UniProt) and Publications
• Organism Name    Chromosome IDs

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These template queries enable the retrieval of database cross references ids (RefSeq <=> Ensembl).

Query for alias and dbxref:

• All Genes    Database Cross References
• Organism    Transcripts + Genes + Database Cross References
• Gene    Database Cross Reference (e.g RefSeq to Ensembl)

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